Source: https://github.com/aipoch/medical-research-skills

When to Use

Converting, validating, or batch-processing mass spectrometry files (e.g., mzML, mzXML, MGF) as part of a pipeline.
Cleaning raw spectra before downstream analysis (smoothing, baseline correction, denoising, peak picking).
Detecting and linking isotope patterns / features for proteomics or metabolomics feature tables.
Running identification-oriented steps where peptide/protein identification integration is required.
Building custom computational MS workflows in Python while leveraging OpenMS algorithms.

Key Features

MS File I/O: Read/write common MS formats (mzML, mzXML, MGF).
Signal Processing: Smoothing, baseline correction, filtering, and peak picking.
Feature Detection: Isotope pattern detection and feature linking utilities.
Identification Support: Hooks for peptide identification workflows via OpenMS-compatible components.
Scripted Workflows: A ready-to-use “Load → Process → Analyze” workflow entry point.